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BAR-Based Multi-Dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscape

preprint
revised on 07.03.2019 and posted on 08.03.2019 by Xiaohui Wang, Qiaole He, Zhaoxi Sun

Construction of free energy landscapes at Quantum mechanics (QM) level is computationally demanding. As shown in previous studies, by employing an indirect scheme (i.e. constructing a thermodynamic cycle connecting QM states via an alchemical pathway), simulations are converged with much less computational burden. The indirect scheme makes QM/ molecular mechanics (MM) free energy simulation orders of magnitude faster than the direct QM/MM schemes. However, the indirect QM/MM simulations were mostly equilibrium sampling based and the nonequilibrium methods were merely exploited in one-dimensional alchemical QM/MM end-state correction at two end states. In this work, we represent a multi-dimensional nonequilibrium pulling scheme for indirect QM/MM free energy simulations, where the whole free energy simulation is performed only with nonequilibrium methods. The collective variable (CV) space we explore is a combination of one alchemical CV and one physically meaningful CV. The current nonequilibrium indirect QM/MM simulation method can be seen as the generalization of equilibrium perturbation based indirect QM/MM methods. The test systems include one backbone dihedral case and one distance case. The two cases are significantly different in size, enabling us to investigate the dependence of the speedup of the indirect scheme on the size of the system. It is shown that the speedup becomes larger when the size of the system becomes larger, which is consistent with the scaling behavior of QM Hamiltonians.

Funding

China scholarship council

History

Email Address of Submitting Author

proszx@163.com

Institution

East China Normal University; Forschungszentrum Juelich; Università della Svizzera italiana

Country

China; Swiss; Germany

ORCID For Submitting Author

0000-0001-8311-7797

Declaration of Conflict of Interest

No conflict of interest.

Version Notes

Identical with the 2nd version. DOI added.

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